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1. Calibrated bagging deep learning for image semantic segmentation: A case study on COVID-19 chest X-ray image

   https://doi.org/10.1371/journal.pone.0276250  

   Nwosu, Lucy; Li, Xiangfang; Qian, Lijun; Kim, Seungchan; Dong, Xishuang (November 2022, PLOS ONE)

   Hemanth, Jude (Ed.)

   Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). Imaging tests such as chest X-ray (CXR) and computed tomography (CT) can provide useful information to clinical staff for facilitating a diagnosis of COVID-19 in a more efficient and comprehensive manner. As a breakthrough of artificial intelligence (AI), deep learning has been applied to perform COVID-19 infection region segmentation and disease classification by analyzing CXR and CT data. However, prediction uncertainty of deep learning models for these tasks, which is very important to safety-critical applications like medical image processing, has not been comprehensively investigated. In this work, we propose a novel ensemble deep learning model through integrating bagging deep learning and model calibration to not only enhance segmentation performance, but also reduce prediction uncertainty. The proposed method has been validated on a large dataset that is associated with CXR image segmentation. Experimental results demonstrate that the proposed method can improve the segmentation performance, as well as decrease prediction uncertainty. 

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2. COVID-FACT: A Fully-Automated Capsule Network-Based Framework for Identification of COVID-19 Cases from Chest CT Scans

   https://doi.org/10.3389/frai.2021.598932  

   Heidarian, Shahin; Afshar, Parnian; Enshaei, Nastaran; Naderkhani, Farnoosh; Rafiee, Moezedin Javad; Babaki Fard, Faranak; Samimi, Kaveh; Atashzar, S. Farokh; Oikonomou, Anastasia; Plataniotis, Konstantinos N.; et al (May 2021, Frontiers in Artificial Intelligence)

   null (Ed.)

   The newly discovered Coronavirus Disease 2019 (COVID-19) has been globally spreading and causing hundreds of thousands of deaths around the world as of its first emergence in late 2019. The rapid outbreak of this disease has overwhelmed health care infrastructures and arises the need to allocate medical equipment and resources more efficiently. The early diagnosis of this disease will lead to the rapid separation of COVID-19 and non-COVID cases, which will be helpful for health care authorities to optimize resource allocation plans and early prevention of the disease. In this regard, a growing number of studies are investigating the capability of deep learning for early diagnosis of COVID-19. Computed tomography (CT) scans have shown distinctive features and higher sensitivity compared to other diagnostic tests, in particular the current gold standard, i.e., the Reverse Transcription Polymerase Chain Reaction (RT-PCR) test. Current deep learning-based algorithms are mainly developed based on Convolutional Neural Networks (CNNs) to identify COVID-19 pneumonia cases. CNNs, however, require extensive data augmentation and large datasets to identify detailed spatial relations between image instances. Furthermore, existing algorithms utilizing CT scans, either extend slice-level predictions to patient-level ones using a simple thresholding mechanism or rely on a sophisticated infection segmentation to identify the disease. In this paper, we propose a two-stage fully automated CT-based framework for identification of COVID-19 positive cases referred to as the “COVID-FACT”. COVID-FACT utilizes Capsule Networks, as its main building blocks and is, therefore, capable of capturing spatial information. In particular, to make the proposed COVID-FACT independent from sophisticated segmentations of the area of infection, slices demonstrating infection are detected at the first stage and the second stage is responsible for classifying patients into COVID and non-COVID cases. COVID-FACT detects slices with infection, and identifies positive COVID-19 cases using an in-house CT scan dataset, containing COVID-19, community acquired pneumonia, and normal cases. Based on our experiments, COVID-FACT achieves an accuracy of 90.82 % , a sensitivity of 94.55 % , a specificity of 86.04 % , and an Area Under the Curve (AUC) of 0.98, while depending on far less supervision and annotation, in comparison to its counterparts. 

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3. Machine-Learning-Enabled Diagnostics with Improved Visualization of Disease Lesions in Chest X-ray Images

   https://doi.org/10.3390/diagnostics14161699  

   Rahman, Md Fashiar; Tseng, Tzu-Liang Bill; Pokojovy, Michael; McCaffrey, Peter; Walser, Eric; Moen, Scott; Vo, Alex; Ho, Johnny C (August 2024, Diagnostics)

   The class activation map (CAM) represents the neural-network-derived region of interest, which can help clarify the mechanism of the convolutional neural network’s determination of any class of interest. In medical imaging, it can help medical practitioners diagnose diseases like COVID-19 or pneumonia by highlighting the suspicious regions in Computational Tomography (CT) or chest X-ray (CXR) film. Many contemporary deep learning techniques only focus on COVID-19 classification tasks using CXRs, while few attempt to make it explainable with a saliency map. To fill this research gap, we first propose a VGG-16-architecture-based deep learning approach in combination with image enhancement, segmentation-based region of interest (ROI) cropping, and data augmentation steps to enhance classification accuracy. Later, a multi-layer Gradient CAM (ML-Grad-CAM) algorithm is integrated to generate a class-specific saliency map for improved visualization in CXR images. We also define and calculate a Severity Assessment Index (SAI) from the saliency map to quantitatively measure infection severity. The trained model achieved an accuracy score of 96.44% for the three-class CXR classification task, i.e., COVID-19, pneumonia, and normal (healthy patients), outperforming many existing techniques in the literature. The saliency maps generated from the proposed ML-GRAD-CAM algorithm are compared with the original Gran-CAM algorithm. 

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4. Lung Pattern Classification Via DCNN

   https://doi.org/10.1109/BigData50022.2020.9378090  

   He, Jing Selena; Han, Meng; Yu, Lei; Mei, Chao (December 2020, Lung Pattern Classification Via DCNN)

   Interstitial lung disease (ILD) causes pulmonary fibrosis. The correct classification of ILD plays a crucial role in the diagnosis and treatment process. In this research work, we propose a lung nodules recognition method based on a deep convolutional neural network (DCNN) and global features, which can be used for computer-aided diagnosis (CAD) of global features of lung nodules. Firstly, a DCNN is constructed based on the characteristics and complexity of lung computerized tomography (CT) images. Then we discussed the effects of different iterations on the recognition results and influence of different model structures on the global features of lung nodules. We also incorporated the improvement of convolution kernel size, feature dimension, and network depth. Thirdly, the effects of different pooling methods, activation functions and training algorithms we proposed has been analyzed to demonstrate the advantages of the new strategy. Finally, the experimental results verify the feasibility of the proposed DCNN for CAD of global features of lung nodules, and the evaluation shown that our proposed method could achieve an outstanding results compare to state-of-arts. 

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5. Undergraduate Research on Physics-Informed Graph Attention Networks for COVID-19 Prediction

   https://doi.org/10.54808/JSCI.20.05.148  

   Liang, Yu; Wu, Dalei (October 2022, Journal of Systemics, Cybernetics and Informatics)

   The COVID-19 pandemic has significantly impacted most countries in the world. Analyzing COVID-19 data from these countries together is a prominent challenge. Under the sponsorship of NSF REU, this paper describes our experience with a ten-week project that aims to guide an REU scholar to develop a physics-guided graph attention network to predict the global COVID- 19 Pandemics. We mainly presented the preparation, implementation, and dissemination of the addressed project. The COVID-19 situation in a country could be dramatically different from that of others, which suggests that COVID-19 pandemic data are generated based on different mechanisms, making COVID-19 data in different countries follow different probability distributions. Learning more than one hundred underlying probability distributions for countries in the world from large scale COVID- 19 data is beyond a single machine learning model. To address this challenge, we proposed two team-learning frameworks for predicting the COVID-19 pandemic trends: peer learning and layered ensemble learning framework. This addressed framework assigns an adaptive physics-guided graph attention network (GAT) to each learning agent. All the learning agents are fabricated in a hierarchical architecture, which enables agents to collaborate with each other in peer-to-peer and cross-layer way. This layered architecture shares the burden of large-scale data processing on machine learning models of all units. Experiments are run to verify the effectiveness of our approaches. The results indicate the proposed ensemble outperforms baseline methods. Besides being documented on GitHub, this work has resulted in two journal papers. 

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